<meta http-equiv="content-type" content="text/html; charset=utf-8"><span class="Apple-style-span" style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)">Hi Lara, I sent an incomplete mail by error :(</span><div>
<span class="Apple-style-span" style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)"><div><br></div><div>I was saying that the simplest way is using vmd.</div><div>Briefly, </div>
<div>1) load the pdb file in vmd. </div><div>2) create a representation using a string like: "same residue as within 3. of protein". </div><div> where "protein" is the group around the molecule you have to use, I used protein just as example</div>
<div> 3. is the cutoff distance between protein and any other ATOM in the system</div><div>3) "same residue" for each atom at point 2) it takes the corresponding residue avoiding residue bracking.</div><div><br>
</div><div><br></div><div>If your pdb is more complex, but you need only water try:</div><div>"water and (same residue as within 3. of protein)".</div><div><br></div><div>Now you can visually inspect your selection and adjusting the distance. </div>
<div><br></div><div><br></div><div>When everything is fine, you can save it through vmd save comman:</div><div>1) in the command line write:</div><div><br></div><div>[atomselect top "same residue as within 3. of protein"] writepdb out.pdb</div>
<div><br></div><div>It should work and it should make the work easier!</div><div><br></div><div>Francesco</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></span><br><br><div class="gmail_quote">
Il giorno 13 aprile 2012 11:38, francesco oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com">francesco.oteri@gmail.com</a>></span> ha scritto:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Lara,<div>the simplest way is using vmd.</div><div>Briefly, </div><div>1) load the pdb file in vmd. </div><div>2) create a representation using a string like: "same residue as within 3. of protein". </div>
<div>
where "protein" is the group around the molecule you have to use, I used protein just as example</div><div><br></div><div><br></div><div><br><br><div class="gmail_quote">Il giorno 13 aprile 2012 11:29, Lara Bunte <span dir="ltr"><<a href="mailto:lara.bunte@yahoo.de" target="_blank">lara.bunte@yahoo.de</a>></span> ha scritto:<div>
<div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="font-size:12pt;font-family:times new roman,new york,times,serif"><div>I read g_select -select 'help all' and I understand nothing of that. <br>
</div><div><br></div><div>In general one have a molecule (valences closed by hydrogen) and a water box around it. How to select only the protein with the first water layers, say one layer? </div><div><br></div><div>Please give me an example how to do this with gromacs. I read the examples in g_select -select 'help all' and I have no Idea what they are talking about. <br>
</div><div><div><br></div><div>Thanks for help</div><div>Greetings</div><div>Lara</div><div><br></div><div><br></div><span></span><div><span></span></div><div><br></div> </div><div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<div style="font-family:times new roman,new york,times,serif;font-size:12pt"> <div dir="ltr"> <font face="Arial"> <hr size="1"><div> <b><span style="font-weight:bold">Von:</span></b> Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<b><span style="font-weight:bold">An:</span></b> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>> <br> </div><b><span style="font-weight:bold">Gesendet:</span></b> 19:26 Mittwoch, 11.April 2012<div>
<br> <b><span style="font-weight:bold">Betreff:</span></b> Re: [gmx-users] File editing - only one layer of water around a molecule<br> </div></font> </div><div><div> <br>On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:<br>
> <br>> <br>> Lara Bunte wrote:<br>>> Could you please give how g_select is used?<br><br>Reading g_select -h might have led you to try g_select -select 'help'<br><br>>> Is there a tutorial for that?<br>
>> <br>> <br>> g_select -select 'help all'<br>> <br>> The information contained therein is very extensive, so be sure to read it thoroughly. It will fill several terminal windows explaining the
syntax and providing examples.<br><br>... and search Google for some examples.<br><br>Mark<br>-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>
</div>